debian/control

@@ -3,7 +3,10 @@ Maintainer: Debian Med Packaging Team <debian-med-packaging@lists.alioth.debian.
 Uploaders: Andreas Tille <tille@debian.org>
 Section: science
 Priority: optional
-Build-Depends: debhelper (>= 12~)
+Build-Depends: debhelper (>= 12~),
+               dh-python,
+               python3,
+               python3-tabulate
 Standards-Version: 4.3.0
 Vcs-Browser: https://salsa.debian.org/med-team/virulencefinder
 Vcs-Git: https://salsa.debian.org/med-team/virulencefinder.git
@@ -11,10 +14,12 @@ Homepage: https://bitbucket.org/genomicepidemiology/virulencefinder
 
 Package: virulencefinder
 Architecture: any
-Depends: ${shlibs:Depends},
-         ${misc:Depends}
+Depends: ${misc:Depends},
+         ${python:Depends},
+         python3,
+         python3-tabulate
 Description: identify viruelnce genes in total or partial sequenced isolates of bacteria
- The VirulenceFinder service contains one python script
+ The VirulenceFinder service contains one Python script
  virulencefinder.py which is the script of the latest version of the
  VirulenceFinder service. VirulenceFinder identifies viruelnce genes in
  total or partial sequenced isolates of bacteria - at the moment only E.

debian/docs

+README*

debian/install

+*.py	usr/share/virulencefinder

debian/links

+usr/share/virulencefinder/virulencefinder.py	usr/bin/virulencefinder.py

debian/lintian-overrides

+# see https://lists.debian.org/debian-med/2018/06/msg00043.html
+virulencefinder: script-with-language-extension usr/bin/*.*

debian/rules

 #!/usr/bin/make -f
 
 # DH_VERBOSE := 1
-export LC_ALL=C.UTF-8
 
-include /usr/share/dpkg/default.mk
-# this provides:
-# DEB_SOURCE: the source package name
-# DEB_VERSION: the full version of the package (epoch + upstream vers. + revision)
-# DEB_VERSION_EPOCH_UPSTREAM: the package's version without the Debian revision
-# DEB_VERSION_UPSTREAM_REVISION: the package's version without the Debian epoch
-# DEB_VERSION_UPSTREAM: the package's upstream version
-# DEB_DISTRIBUTION: the distribution(s) listed in the current entry of debian/changelog
-# SOURCE_DATE_EPOCH: the source release date as seconds since the epoch, as
-#                    specified by <https://reproducible-builds.org/specs/source-date-epoch/>
-
-# for hardening you might like to uncomment this:
-# export DEB_BUILD_MAINT_OPTIONS=hardening=+all
+export PYBUILD_SYSTEM=custom
+export PYBUILD_CLEAN_ARGS=rm -rf test/results_tab.tsv
 
 %:
-	dh $@
+	dh $@ --with python3 --buildsystem=pybuild
 
-### When overriding auto_test make sure DEB_BUILD_OPTIONS will be respected
-#override_dh_auto_test:
+override_dh_auto_test:
 #ifeq (,$(filter nocheck,$(DEB_BUILD_OPTIONS)))
-#	do_stuff_for_testing
+	./virulencefinder.py -i test/test.fsa -o test/ -mp blastn -x -q ; \
+	file=test/results_tab.tsv ; \
+	DIFF=$$(diff $file test/test_results.tsv) ; \
+	if [ "$DIFF" == "" ] && [ -s $file ] ; then \
+	    echo "TEST SUCCEEDED" ; \
+	else \
+	   echo "TEST FAILED"; \
+	fi
 #endif
-
-### If you **really** can not use uscan (even not with mode=git) use a debian/get-orig-script
-#get-orig-source:
-#	. debian/get-orig-source

debian/upstream/metadata

+Reference:
+  Author: Katrine Grimstrup Joensen and Flemming Scheutz and Ole Lund and Henrik Hasman and Rolf S. Kaas and Eva M. Nielsen and Frank M. Aarestrup
+  Title: Real-Time Whole-Genome Sequencing for Routine Typing, Surveillance, and Outbreak Detection of Verotoxigenic Escherichia coli
+  Journal: Journal of Clinical Microbiology
+  Year: 2014
+  Volume: 52
+  Number: 5
+  Pages: 1501-10
+  DOI: 10.1128/JCM.03617-13
+  PMID: 24574290
+  URL: https://jcm.asm.org/content/52/5/1501
+  eprint: https://jcm.asm.org/content/jcm/52/5/1501.full-text.pdf